Installation#

Requirements#

Biotite requires a modern Python installation (at least the last two years are supported) and the following packages:

  • numpy

  • requests

  • msgpack

  • networkx

Installation of the biotite package will also automatically install these dependencies if not already present.

Some functionalities require extra packages:

  • matplotlib - Required for plotting purposes.

Installation from PyPI#

Biotite is available as wheels for a variety of platforms (Windows, Linux, OS X). Simply type

$ pip install biotite

If pip finds an appropriate wheel for your system configuration on PyPI, it will download and install it. If no fitting wheel is found, pip will fall back to the source distribution. In this case, installation will take longer, because extension modules need to be compiled first. Note that this requires a C-compiler (typically GCC) installed on your system.

Installation via Conda#

Biotite is also available via Conda.

$ conda install -c conda-forge biotite

Installation from source#

You can also install Biotite from the project repository. However, in addition to building and installing the package, the internal Chemical Component Dictionary (CCD). for biotite.structure.info needs to be built with the setup_ccd module. The script in turn requires Biotite. The solution to this chicken-and-egg problem is to first install Biotite without the CCD and build the CCD afterwards. After cloning the repository, navigate to its top-level directory (the one setup.py is in) and type the following:

$ pip install .
$ python -m biotite.setup_ccd

setup_ccd.py can also be used to update the internal CCD to the current upstream version from the PDB.

Having the Biotite installation always pointing to your repository clone is also possible. Substitute the installation with the following commands instead:

$ pip install -e .
$ python -m biotite.setup_ccd

Common issues and solutions#

Compiler error when building Biotite#

There is a known problem with GCC compiler errors in some Linux distributions (e.g. Arch Linux) when building Biotite from source. Among other error lines the central error is the following:

unable to initialize decompress status for section .debug_info

While the exact reason for this error is still unknown, this can be fixed by using a GCC installed via Conda:

$ conda install -c conda-forge c-compiler

ValueError when importing Biotite#

When importing one of Biotite’s subpackages one of the following errors might occur:

ValueError: numpy.ufunc size changed, may indicate binary incompatibility.
ValueError: numpy.ndarray size changed, may indicate binary incompatibility.

The reason for this error is, that Biotite was built against a NumPy version other than the one installed. This happens for example when NumPy is updated, but Biotite is already installed. Try updating NumPy and Biotite to solve this issue.